BioC 3.3: CHECK report for OmicsMarkeR on windows2.bioconductor.org

Package: OmicsMarkeR

Version: 1.3.0

Command: rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.3.0.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.3.0.tar.gz

StartedAt: 2015-10-27 04:43:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:49:26 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 378.6 seconds

RetCode: 0

Status:  OK

CheckDir: OmicsMarkeR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && mkdir OmicsMarkeR.buildbin-libdir OmicsMarkeR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.3.0.tar.gz >OmicsMarkeR.Rcheck\00install.out 2>&1 && cp OmicsMarkeR.Rcheck\00install.out OmicsMarkeR-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=OmicsMarkeR.buildbin-libdir --install="check:OmicsMarkeR-install.out" --force-multiarch --no-vignettes --timings OmicsMarkeR_1.3.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/OmicsMarkeR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicsMarkeR/DESCRIPTION' ... OK
* this is package 'OmicsMarkeR' version '1.3.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'OmicsMarkeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
perm.class: no visible binding for global variable 'outIndex'
Undefined global functions or variables:
  outIndex
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [79s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
performance.metrics 13.38   0.05   13.42
perm.class          12.52   0.00   12.52
predictNewClasses   12.42   0.02   12.44
perm.features       11.33   0.01   11.35
feature.table       11.07   0.06   11.76
fs.stability         9.95   0.08   10.03
** running examples for arch 'x64' ... [83s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
performance.metrics 13.84   0.00   14.01
perm.class          13.62   0.04   13.66
predictNewClasses   12.18   0.00   12.21
perm.features       12.11   0.01   12.13
feature.table       11.61   0.03   11.64
fs.stability        11.44   0.01   11.46
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [57s]
 [57s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [67s]
 [67s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/OmicsMarkeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'OmicsMarkeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'OmicsMarkeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicsMarkeR' as OmicsMarkeR_1.3.0.zip
* DONE (OmicsMarkeR)

name	user	system	elapsed
RPT	0.00	0.00	0.58
aggregation	0	0	0
canberra	0	0	0
canberra_stability	0	0	0
create.corr.matrix	0.01	0.00	0.02
create.discr.matrix	0.02	0.00	0.01
create.random.matrix	0	0	0
denovo.grid	0.01	0.00	0.02
feature.table	11.07	0.06	11.76
fit.only.model	4.51	0.08	4.60
fs.ensembl.stability	0	0	0
fs.stability	9.95	0.08	10.03
jaccard	0	0	0
kuncheva	0	0	0
modelList	0	0	0
ochiai	0	0	0
pairwise.model.stability	0.02	0.00	0.02
pairwise.stability	0.01	0.00	0.02
params	0	0	0
performance.metrics	13.38	0.05	13.42
perm.class	12.52	0.00	12.52
perm.features	11.33	0.01	11.35
pof	0	0	0
predictNewClasses	12.42	0.02	12.44
sorensen	0	0	0
spearman	0	0	0
svmrfeFeatureRanking	0.07	0.00	0.06
svmrfeFeatureRankingForMulticlass	0.12	0.00	0.12

name	user	system	elapsed
RPT	0	0	0
aggregation	0	0	0
canberra	0	0	0
canberra_stability	0	0	0
create.corr.matrix	0	0	0
create.discr.matrix	0	0	0
create.random.matrix	0.02	0.00	0.01
denovo.grid	0	0	0
feature.table	11.61	0.03	11.64
fit.only.model	4.64	0.00	4.64
fs.ensembl.stability	0	0	0
fs.stability	11.44	0.01	11.46
jaccard	0	0	0
kuncheva	0	0	0
modelList	0	0	0
ochiai	0	0	0
pairwise.model.stability	0.02	0.00	0.02
pairwise.stability	0	0	0
params	0	0	0
performance.metrics	13.84	0.00	14.01
perm.class	13.62	0.04	13.66
perm.features	12.11	0.01	12.13
pof	0	0	0
predictNewClasses	12.18	0.00	12.21
sorensen	0	0	0
spearman	0	0	0
svmrfeFeatureRanking	0.08	0.00	0.08
svmrfeFeatureRankingForMulticlass	0.14	0.00	0.14